Brain data

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

--2022-06-14 13:34:29--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210726/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.114.4
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Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T133429Z&X-Amz-Expires=300&X-Amz-Signature=ae1f7871012dac0e29c9d3eee5d5ac3bbdcacb05a98e81423614952c9600a988&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2022-06-14 13:34:29--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/8209c733-4891-4342-8c30-ccd075b128f8?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220614%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220614T133429Z&X-Amz-Expires=300&X-Amz-Signature=ae1f7871012dac0e29c9d3eee5d5ac3bbdcacb05a98e81423614952c9600a988&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
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Length: 939721 (918K) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  5% 41.7M 0s
    50K .......... .......... .......... .......... .......... 10% 82.3M 0s
   100K .......... .......... .......... .......... .......... 16% 72.0M 0s
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   350K .......... .......... .......... .......... .......... 43%  158M 0s
   400K .......... .......... .......... .......... .......... 49%  120M 0s
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   850K .......... .......... .......... .......... .......... 98%  181M 0s
   900K .......... .......                                    100%  108M=0.008s

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Archive:  neuromod-anat-brain-qmri.zip
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Load data plot it

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain gray matter qMRI microstructure'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI

fig_wm = Plot(dataset, plot_name = 'brain-2')

fig_wm.title = 'Brain white matter qMRI microstructure'

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')